Jie Zheng
Orcid: 0000-0001-6774-9786Affiliations:
- ShanghaiTech University, School of Information Science and Technology, Shanghai, China
- Nanyang Technological University, School of Computer Engineering, Bioinformatics Research Centre, Singapore
- A*STAR, Genome Institute of Singapore, Singapore
- National Institutes of Health, Bethesda, MD, USA (2006 - 2011)
- University of California Riverside, CA, USA (PhD 2006)
According to our database1,
Jie Zheng
authored at least 71 papers
between 2004 and 2024.
Collaborative distances:
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Bibliography
2024
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality.
Bioinform., February, 2024
TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities.
Bioinform., January, 2024
2023
Bioinform., 2023
2022
Prediction of gene co-expression from chromatin contacts with graph attention network.
Bioinform., 2022
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery.
Database J. Biol. Databases Curation, 2022
2021
BMC Bioinform., 2021
PIKE-R2P: Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction.
BMC Bioinform., 2021
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers.
Bioinform., 2021
Graph contextualized attention network for predicting synthetic lethality in human cancers.
Bioinform., 2021
Predicting Synthetic Lethality in Human Cancers via Multi-Graph Ensemble Neural Network.
Proceedings of the 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society, 2021
2020
Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018).
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
SL<sup>2</sup>MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
A Monte Carlo method for <i>in silico</i> modeling and visualization of Waddington's epigenetic landscape with intermediate details.
Biosyst., 2020
2019
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019
Genome Analysis - Identification of Genes Involved in Host-Pathogen Protein-Protein Interaction Networks.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019
Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus.
BMC Syst. Biol., 2019
An Encoding Scheme Capturing Generic Priors and Properties of Amino Acids Improves Protein Classification.
IEEE Access, 2019
2018
Computational identification of physicochemical signatures for host tropism of influenza A virus.
J. Bioinform. Comput. Biol., 2018
Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease.
BMC Syst. Biol., 2018
Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.
BMC Genom., 2018
Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes.
BMC Bioinform., 2018
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks.
Bioinform., 2018
2017
BMC Syst. Biol., 2017
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape.
Bioinform., 2017
NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential.
Bioinform., 2017
Identification of Potential Critical Virulent Sites Based on Hemagglutinin of Influenza a Virus in Past Pandemic Strains.
Proceedings of the 6th International Conference on Bioinformatics and Biomedical Science, 2017
Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
2016
The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.
Nucleic Acids Res., 2016
Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation.
BMC Syst. Biol., 2016
Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways.
BMC Syst. Biol., 2016
Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016
TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016
2015
Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates.
J. Bioinform. Comput. Biol., 2015
Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity.
BMC Syst. Biol., 2015
Improving compound-protein interaction prediction by building up highly credible negative samples.
Bioinform., 2015
Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development.
Bioinform., 2015
2014
Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining.
Comput. Biol. Chem., 2014
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast.
BMC Syst. Biol., 2014
BMC Syst. Biol., 2014
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.
BMC Bioinform., 2014
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.
BMC Bioinform., 2014
BMC Bioinform., 2014
CUDAGRN: Parallel Speedup of Inferring Large Gene Regulatory Networks from Expression Data Using Random Forest.
Proceedings of the Pattern Recognition in Bioinformatics, 2014
Proceedings of the International Conference on Big Data and Smart Computing, BIGCOMP 2014, 2014
Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014
2013
Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K.
BMC Bioinform., 2013
Bioinform., 2013
Inferring Gene Regulatory Networks from Time-Series Expressions Using Random Forests Ensemble.
Proceedings of the Pattern Recognition in Bioinformatics, 2013
Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression.
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013
Integrating epigenetic prior in dynamic Bayesian network for gene regulatory network inference.
Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2013
Syn-Lethality: An integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer.
Proceedings of the ACM Conference on Bioinformatics, 2013
2012
Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression.
PLoS Comput. Biol., 2012
Proceedings of the 11th International Workshop on Data Mining in Bioinformatics, 2012
NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots.
Proceedings of the ACM International Conference on Bioinformatics, 2012
Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse.
Proceedings of the ACM International Conference on Bioinformatics, 2012
2011
Integration of Epigenetic Data in Bayesian Network Modeling of Gene Regulatory Network.
Proceedings of the Pattern Recognition in Bioinformatics, 2011
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011
2010
Bioinform., 2010
2009
The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis.
BMC Syst. Biol., 2009
2007
A Rigorous Analysis of the Pattern of Intron Conservation Supports the <i>Coelomata</i> Clade of Animals.
Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007
2006
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.
BMC Bioinform., 2006
2005
IEEE ACM Trans. Comput. Biol. Bioinform., 2005
Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005
2004
Bioinform., 2004